The joint effects of background selection and genetic recombination on local gene genealogies

Genetics

Volumn 189, Issue 1, 2011, Pages 251-266

  Zeng, Kai ^a   Charlesworth, Brian ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; DNA SEQUENCE; GENE MUTATION; GENEALOGY; GENETIC LINKAGE; GENETIC MODEL; GENETIC POLYMORPHISM; GENETIC RECOMBINATION; GENETIC SELECTION; MODEL; PRIORITY JOURNAL; SIMULATION;

EID: 80052650680     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.111.130575     Document Type: Article

References (68)

1. Aguadé, M., N. Miyashita, and C. H. Langley, 1989 Reduced variation in the yellow-achaete-scute region in natural populations of Drosophila melanogaster. Genetics 122: 607-615.
2. Andolfatto, P., 2007 Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome. Genome Res. 17: 1755-1762.
3. Begun, D. J., and C. F. Aquadro, 1992 Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature 356: 519-520.
4. Berry, A. J., J. W. Ajioka, and M. Kreitman, 1991 Lack of polymorphism on the Drosophila fourth chromosome resulting from selection. Genetics 129: 1111-1117.
5. Betancourt, A. J., and D. C. Presgraves, 2002 Linkage limits the power of natural selection in Drosophila. Proc. Natl. Acad. Sci. USA 99: 13616-13620.
6. Betancourt, A. J., J. J. Welch, and B. Charlesworth, 2009 Reduced effectiveness of selection caused by a lack of recombination. Curr. Biol. 19: 655-660.
7. Boyko, A. R., S. H. Williamson, A. R. Indap, J. D. Degenhardt, R. D. Hernandez et al., 2008 Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet. 4: e1000083.
8. Cai, J. J., J. M. Macpherson, G. Sella, and D.A. Petrov, 2009 Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genet. 5: e1000336.
9. Charlesworth, B., 1990 Mutation-selection balance and the evolutionary advantage of sex and recombination. Genet. Res. 55: 199-221.
10. Charlesworth, B., 1994 The effect of background selection against deleterious mutations on weakly selected, linked variants. Genet. Res. 63: 213-227.
11. Charlesworth, B., 1996 Background selection and patterns of genetic diversity in Drosophila melanogaster. Genet. Res. 68: 131-149.
12. Charlesworth, B., M. T. Morgan, and D. Charlesworth, 1993 The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289-1303.
13. Charlesworth, B., A. J. Betancourt, V. B. Kaiser, and I. Gordo, 2009 Genetic recombination and molecular evolution. Cold Spring Harbor Symp. Quant. Biol. 74: 177-186.
14. Charlesworth, D., B. Charlesworth, and M. T. Morgan, 1995 The pattern of neutral molecular variation under the background selection model. Genetics 141: 1619-1632.
15. Comeron, J. M., and T. B. Guthrie, 2005 Intragenic Hill-Robertson interference influences selection intensity on synonymous mutations in Drosophila. Mol. Biol. Evol. 22: 2519-2530.
16. Comeron, J. M., and M. Kreitman, 2002 Population, evolutionary and genomic consequences of interference selection. Genetics 161: 389-410.
17. Cutter, A. D., and J. Y. Choi, 2010 Natural selection shapes nucleotide polymorphism across the genome of the nematode Caenorhabditis briggsae. Genome Res. 20: 1103-1111.
18. Ewens, W. J., 2004 Mathematical Population Genetics. Springer-Verlag, Berlin.
19. Fisher, R. A., 1930 The Genetical Theory of Natural Selection. Clarendon Press, Oxford.
20. Fu, Y. X., 1997 Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915-925.
21. Fu, Y. X., 2006 Exact coalescent for the Wright-Fisher model. Theor. Popul. Biol. 69: 385-394.
22. Fu, Y. X., and W. H. Li, 1993 Statistical tests of neutrality of mutations. Genetics 133: 693-709.
23. Gordo, I., A. Navarro, and B. Charlesworth, 2002 Muller's ratchet and the pattern of variation at a neutral locus. Genetics 161: 835-848.
24. Griffiths, R. C., 1981 Neutral two-locus multiple allele models with recombination. Theor. Popul. Biol. 19: 169-186.
25. Haddrill, P. R., D. L. Halligan, D. Tomaras, and B. Charlesworth, 2007 Reduced efficacy of selection in regions of the Drosophila genome that lack crossing over. Genome Biol. 8: R18.
26. Haddrill, P. R., K. Zeng, and B. Charlesworth, 2011 Determinants of synonymous and nonsynonymous variability in three species of Drosophila. Mol. Biol. Evol. 28: 1731-1743.
27. Haigh, J., 1978 The accumulation of deleterious genes in a population-Muller's Ratchet. Theor. Popul. Biol. 14: 251-267.
28. Hammer, M. F., A. E. Woerner, F. L. Mendez, J. C. Watkins, M. P. Cox et al., 2010 The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes. Nat. Genet. 42: 830-831.
29. Hey, J., and R. M. Kliman, 2002 Interactions between natural selection, recombination and gene density in the genes of Drosophila. Genetics 160: 595-608.
30. Hudson, R. R., 1990 Gene genealogies and the coalescent process. Oxford Surv. Evol. Biol. 7: 1-44.
31. Hudson, R. R., 2002 Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
32. Hudson, R. R., and N. L. Kaplan, 1994 Gene trees with background selection, pp. 140-153 in Non-Neutral Evolution: Theories and Molecular Data, edited by Golding, B.Chapman & Hall, London.
33. Hudson, R. R., and N. L. Kaplan, 1995 Deleterious background selection with recombination. Genetics 141: 1605-1617.
34. Johnson, T., 1999 The approach to mutation-selection balance in an infinite asexual population, and the evolution of mutation rates. Proc. Biol. Sci. B 266: 2389-2397.
35. Kaiser, V. B., and B. Charlesworth, 2009 The effects of deleterious mutations on evolution in non-recombining genomes. Trends Genet. 25: 9-12.
36. Keightley, P. D., and A. Eyre-Walker, 2007 Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies. Genetics 177: 2251-2261.
37. Kimura, M., 1969 The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics 61: 893-903.
38. Kimura, M., and T. Maruyama, 1966 The mutational load with epistatic gene interactions in fitness. Genetics 54: 1337-1351.
39. Kingman, J. F. C., 1982 On the genealogy of large populations. J. Appl. Probab. 19A: 27-43.
40. Kreitman, M., 1983 Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster. Nature 304: 412-417.
41. Larracuente, A. M., T. B. Sackton, A. J. Greenberg, A. Wong, N. D. Singh et al., 2008 Evolution of protein-coding genes in Drosophila. Trends Genet. 24: 114-123.
42. Loewe, L., and B. Charlesworth, 2006 Inferring the distribution of mutational effects on fitness in Drosophila. Biol. Lett. 2: 426-430.
43. Loewe, L., and B. Charlesworth, 2007 Background selection in single genes may explain patterns of codon bias. Genetics 175: 1381-1393.
44. Maynard Smith, J., and J. Haigh, 1974 The hitch-hiking effect of a favourable gene. Genet. Res. 23: 23-35.
45. McVean, G. A., 2002 A genealogical interpretation of linkage disequilibrium. Genetics 162: 987-991.
46. McVicker, G., D. Gordon, C. Davis, and P. Green, 2009 Widespread genomic signatures of natural selection in hominid evolution. PLoS Genet. 5: e1000471.
47. Neuhauser, C., and S. M. Krone, 1997 The genealogy of samples in models with selection. Genetics 145: 519-534.
48. Nordborg, M., B. Charlesworth, and D. Charlesworth, 1996 The effect of recombination on background selection. Genet. Res. 67: 159-174.
49. O'Fallon, B. D., J. Seger, and F. R. Adler, 2010 A continuous-state coalescent and the impact of weak selection on the structure of gene genealogies. Mol. Biol. Evol. 27: 1162-1172.
50. Presgraves, D. C., 2005 Recombination enhances protein adaptation in Drosophila melanogaster. Curr. Biol. 15: 1651-1656.
51. Rockman, M. V., S. S. Skrovanek, and L. Kruglyak, 2010 Selection at linked sites shapes heritable phenotypic variation in C. elegans. Science 330: 372-376.
52. Santiago, E., and A. Caballero, 1998 Effective size and polymorphism of linked neutral loci in populations under directional selection. Genetics 149: 2105-2117.
53. Seger, J., W. A. Smith, J. J. Perry, J. Hunn, Z. A. Kaliszewska et al., 2010 Gene genealogies strongly distorted by weakly interfering mutations in constant environments. Genetics 184: 529-545.
54. Sella, G., D. A. Petrov, M. Przeworski, and P. Andolfatto, 2009 Pervasive natural selection in the Drosophila genome? PLoS Genet. 5: e1000495.
55. Shapiro, J. A., W. Huang, C. Zhang, M. J. Hubisz, J. Lu et al., 2007 Adaptive genic evolution in the Drosophila genomes. Proc. Natl. Acad. Sci. USA 104: 2271-2276.
56. Shnol, E. E., and A. S. Kondrashov, 1993 The effect of selection on the phenotypic variance. Genetics 134: 995-996.
57. Simmons, M. J., and J. F. Crow, 1977 Mutations affecting fitness in Drosophila populations. Annu. Rev. Genet. 11: 49-78.
58. Stephan, W., 1995 An improved method for estimating the rate of fixation of favorable mutations based on DNA polymorphism data. Mol. Biol. Evol. 12: 959-962.
59. Stephan, W., B. Charlesworth, and G. McVean, 1999 The effect of background selection at a single locus on weakly selected, partially linked variants. Genet. Res. 73: 133-146.
60. Tajima, F., 1983 Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437-460.
61. Tajima, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
62. Wakeley, J., 2008a Coalescent Theroy: An Introduction. Roberts & Company, Greenwood Village.
63. Wakeley, J., 2008b Conditional gene genealogies under strong purifying selection. Mol. Biol. Evol. 25: 2615-2626.
64. Watterson, G. A., 1975 On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7: 256-276.
65. Williamson, S., and M. E. Orive, 2002 The genealogy of a sequence subject to purifying selection at multiple sites. Mol. Biol. Evol. 19: 1376-1384.
66. Wright, S. I., and P. Andolfatto, 2008 The impact of natural selection on the genome: emerging patterns in Drosophila and Arabidopsis. Annu. Rev. Ecol. Evol. Syst. 39: 193-213.
67. Zeng, K., and B. Charlesworth, 2010 The effects of demography and linkage on the estimation of selection and mutation parameters. Genetics 186: 1411-1424.
68. Zeng, K., Y. X. Fu, S. Shi, and C. I. Wu, 2006 Statistical tests for detecting positive selection by utilizing high-frequency variants. Genetics 174: 1431-1439.